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The recently orphaned Mary Lennox is sent from her home in India to her uncle Lord Archibald Craven's mansion, Misselthwaite Manor, in Yorkshire, England. Unloved and neglected by her late parents, who had just been killed in an earthquake, she is a cold, unpleasant girl, unhappy in her new surroundings. Head housekeeper Mrs. Medlock informs Mary she will not be spoiled as she was in India and that her uncle, who spends extended periods of time away from the Manor, will likely not see her. Mary is ordered not to leave her room, but strange noises lead her to explore the mansion on her own. Mrs. Medlock eventually allows her to play outside to keep her from poking about the house. In the expansive grounds of the Manor, Mary discovers her late aunt's garden, which was locked and neglected since her accidental death ten years prior.

Martha Sowerby, a maid, and her brother, Dickon, a nature-loving boy who can "talk" to animals, befriend Mary. Fascinated by the "secret garden," Mary enlists Dickon to help her bring it back to life, gradually losing her sour persona and becoming a more friendly, happy child in the process. When finally introduced to her uncle, Mary is apprehensive, knowing he was responsible for locking up the secret garden. Fearful he would do it again, Mary evasively asks to plant seeds in an "unwanted" part of the Manor, to which Lord Craven grants permission before leaving the country for the rest of the year. Confident that the garden will remain a secret, Mary and Dickon continue their work.

Hidden away in the gloomy mansion is Mary's cousin, Colin, who has been treated all his life like a fragile, sickly invalid. This has turned him into a demanding, short tempered, helpless boy who has never left his room or learned to walk. Mary eventually discovers Colin and learns the strange noises she has been hearing is him crying. She is taken aback by his difficult nature, but reaches out to him anyway. She shows him that he's not actually sick, and that the outside world is not as dangerous as Mrs. Medlock, who is in charge of caring for him, claims. Encouraged by Mary, Colin decides to go outside for the first time in his life. Mary and Dickon take him to the secret garden and Colin begins his own healing process.

Colin, Mary, and Dickon spend all of their time in the garden, where Colin learns to both stand and walk on his own. Anxious to show Colin's new-found life to his father, they perform a "magic" ceremony in hopes to bring him back home. It appears to work, as Lord Craven awakens suddenly from a dream of his late wife calling him home. He immediately returns to Yorkshire. He discovers Colin walking and playing upon his return, which leaves him dumbfounded with joy. Mary runs off and breaks down in tears, fearful that both she and the garden will be neglected and locked away again. Her uncle reassures her that she is part of the family and promises to never lock the garden up again. He thanks her for bringing his family back to life; they embrace, and then celebrate with Colin, Dickon, and the Manor staff. The film concludes with Mary reflecting in voiceover that "if you look the right way, the whole world is a garden."